[gmx-users] rigid tetrahedral molecule
msanku65 at yahoo.com
Thu Apr 28 03:12:50 CEST 2011
I am interested in simulating a anionic molecule BF4(-) ( Boron
tetrafluoride). In the paper which developed the parameters for this molecule,
it is mentioned that it has been used as 'rigid' molecule i.e the molecule only
has non-bonding interaction but there was no intramolecular motion as the
geometry was fixed.
I am trying to simulate this molecule in gromacs treating it as rigid. But, I
was looking for best way to 'rigidify' this molecule.
I was wondering whether using LINCS to constrain all B-F and F-F bonds will be
good enough . Or, Should I use virtual sites ? If I really need to use virtual
site, will it be something like TIP5P water model ?
Can someone suggest the best wayout ?
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